add fix for reading dbj features and underscores in accession numbers

broadinstitute · Nov 27, 2018 · a32be51 · a32be51
1 parent ad9a6ce
commit a32be51
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/util/genbank.py b/util/genbank.py
@@ -36,7 +36,7 @@ def get_feature_table_id(featureTableFile):
                 if not (
                     (seqid.startswith('gb|') or seqid.startswith('ref|'))):
                     raise Exception("reference annotation ID does not appear to refer to a GenBank or RefSeq accession: %s" % seqid)
-                m = re.search(r"(?P<db>(?:gb|ref))\|(?:(?P<accession>[a-zA-Z0-9\.]+))+.*", seqid)
+                m = re.search(r"(?P<db>(?:gb|ref|dbj))\|(?:(?P<accession>[a-zA-Z0-9\._]+))+.*", seqid)
                 if m:
                    seqid = m.group("accession")
                 else: